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1 <?xml version="1.0" ?>
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2 <tool id="qiime_gneiss_assign-ids" name="qiime gneiss assign-ids"
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3 version="2020.8">
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4 <description>Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime gneiss assign-ids
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10
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11 --i-input-table=$iinputtable
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12
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13 --i-input-tree=$iinputtree
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15 --o-output-table=ooutputtable
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16
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17 --o-output-tree=ooutputtree
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18
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19 #if str($examples) != 'None':
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20 --examples=$examples
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21 #end if
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22
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23 ;
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24 cp ooutputtree.qza $ooutputtree
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25
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26 ]]></command>
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27 <inputs>
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28 <param format="qza,no_unzip.zip" label="--i-input-table: ARTIFACT FeatureTable[Frequency] The input table of counts. [required]" name="iinputtable" optional="False" type="data" />
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29 <param format="qza,no_unzip.zip" label="--i-input-tree: ARTIFACT Phylogeny[Rooted] The input tree with potential missing ids. [required]" name="iinputtree" optional="False" type="data" />
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30 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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31
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32 </inputs>
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33
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34 <outputs>
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35 <data format="qza" label="${tool.name} on ${on_string}: outputtable.qza" name="ooutputtable" />
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36 <data format="qza" label="${tool.name} on ${on_string}: outputtree.qza" name="ooutputtree" />
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37
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38 </outputs>
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39
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40 <help><![CDATA[
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41 Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.
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42 ###############################################################
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43
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44
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45 Assigns UUIDs to uniquely identify internal nodes in the tree. Also
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46 corrects for polytomies to create strictly bifurcating trees and aligns the
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47 table columns with the tree tip names
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48
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49 Parameters
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50 ----------
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51 input_table : FeatureTable[Frequency]
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52 The input table of counts.
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53 input_tree : Phylogeny[Rooted]
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54 The input tree with potential missing ids.
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55
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56 Returns
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57 -------
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58 output_table : FeatureTable[Frequency]
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59 A table with features matching the tree tips.
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60 output_tree : Hierarchy
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61 A tree with uniquely identifying ids.
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62 ]]></help>
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63 <macros>
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64 <import>qiime_citation.xml</import>
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65 </macros>
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66 <expand macro="qiime_citation"/>
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67 </tool> |
